Novel Ubiquitin-Conjugating Enzyme

Experimental Data Snapshot

  • Resolution: 2.18 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.

Sheng, Y.Hong, J.H.Doherty, R.Srikumar, T.Shloush, J.Avvakumov, G.V.Walker, J.R.Xue, S.Neculai, D.Wan, J.W.Kim, S.K.Arrowsmith, C.H.Raught, B.Dhe-Paganon, S.

(2012) Mol Cell Proteomics 11: 329-341

  • DOI: https://doi.org/10.1074/mcp.O111.013706
  • Primary Citation of Related Structures:  
    1Y6L, 1YH2, 1YRV, 1ZDN, 1ZUO, 2A4D, 2A7L, 2AWF, 2F4W, 2OB4, 2QGX, 2Z5D, 3BZH, 3CEG

  • PubMed Abstract: 

    Here we describe a systematic structure-function analysis of the human ubiquitin (Ub) E2 conjugating proteins, consisting of the determination of 15 new high-resolution three-dimensional structures of E2 catalytic domains, and autoubiquitylation assays for 26 Ub-loading E2s screened against a panel of nine different HECT (homologous to E6-AP carboxyl terminus) E3 ligase domains. Integration of our structural and biochemical data revealed several E2 surface properties associated with Ub chain building activity; (1) net positive or neutral E2 charge, (2) an "acidic trough" located near the catalytic Cys, surrounded by an extensive basic region, and (3) similarity to the previously described HECT binding signature in UBE2L3 (UbcH7). Mass spectrometry was used to characterize the autoubiquitylation products of a number of functional E2-HECT pairs, and demonstrated that HECT domains from different subfamilies catalyze the formation of very different types of Ub chains, largely independent of the E2 in the reaction. Our data set represents the first comprehensive analysis of E2-HECT E3 interactions, and thus provides a framework for better understanding the molecular mechanisms of ubiquitylation.

  • Organizational Affiliation

    Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ubiquitin-conjugating ligase MGC351130169Homo sapiensMutation(s): 0 
Gene Names: MGC35130
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VVX9 (Homo sapiens)
Explore Q5VVX9 
Go to UniProtKB:  Q5VVX9
GTEx:  ENSG00000177414 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5VVX9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.18 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.244 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.968α = 90
b = 74.009β = 90
c = 119.733γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-11-28
    Changes: Database references
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-08-23
    Changes: Data collection, Database references, Refinement description